The Iron Agent
by captaincoulson18
Summary: Coulson and team are visited by a certain genius-billionaire-playboy-phillanthropist...
1. Chapter 1

AN: Takes place after ep. 6 and slightly AU: The epilogue to this story will be posted tomorrow

Tony stark because of reasons

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><p>To say Agent Coulson was tired would be the understatement of the century. Phil Coulson was flat out exhausted.<p>

Another piece of alien tech had shown up; this time a kid who had been visiting New York during the attack had brought a piece of Chitauri armor he had found to school for show and tell, and had subsequently caused an entire school community to become hypnotized into attacking each other. Long story short, it was a giant, giant mess. Technically, this was not even the type of small-scale stuff Coulson and his team were supposed to be dealing with, but it had been such a huge catastrophe that they had been called in anyway, and the entire team, still burned and on edge from their last mission had to work double-time to clean up the mess. No one was happy to work, and it wasn't a pleasant situation.

Finally, when the antiserum had been discovered and the crisis cleaned up, the team was finally able to rest. They had just touched down at a SHIELD base just outside of Cincinnati, and Coulson had changed into his Captain America Shield pajama pants and was drifting off when he suddenly heard a knock on his door.

"Um, Agent Coulson," Came Simmons's nervous voice. "We have a bit of a situation."

Coulson had specifically told the team to only wake him up if a. someone was dying, b. the plane was on fire or c. if Nick Fury himself was on the aircraft, so he hoped for their sake that this was one hell of a situation. He sighed, threw off his covers, and went to unlock the door.

"Hello Agent Simmons, who's dying?" Simmons, startled by seeing Coulson in his pajamas, stuttered a bit before answering.

"Um…Uh…N-nobody is dying sir…it's...it's just that we have unexpected visitors…." Coulson raised one of his eyebrows.

"Unexpected visitors? Who the hell is visiting us? Is it Fury?"

"No sir, but he's just as important."

"Who is it, Simmons? Please hurry. As you can see, I was kind of in the middle of something…" He said, motioning to his pajamas.

"Yes, indeed, sir. It's…it's Tony Stark sir. And his assistant, Ms. Potts."

Shit.

"Tony Stark!? Where is he now?"

"Fitz is showing him around the lab…and he's making fun of Ward. He's actually quite funny…."

"Don't you tell me about Tony Stark being funny…I'll be right there, Simmons, I just have to get changed." He said, shooing her out of the room and making his way over to the closet. He jumped into a suit and then ran downstairs. His mind was racing. Tony Stark was not supposed to know about him being alive. The Avengers were definitely not level 7. Did Fury even know about this? And oh boy, if that Asgardian crackpot didn't kill him, you could be sure Pepper Potts was going to.

Still, he couldn't help smile when he though about seeing his old friend once again. But would she even still want to be friends with him? Not only had he declined to alert her about not being dead, but he had changed since they had last met…

He barely had time to think about this, because before he knew it, he was down at the lab. The moment he opened the door, Stark broke the conversation he was having with Fitz and looked Coulson dead in the eye.

"Well, well, do my eyes deceive me? The fantastic Agent Coulson. In the living flesh, back from the dead."

"Hello, Mr. Stark."

"Bring it in, Agent, bring it in," And before the agent could protest, Stark had wrapped him in the biggest bro-hug that had ever been given. The moment he let go, Phil barely had time to gather himself when he was attacked by something even scarier than Tony Stark: an upset Pepper Potts. She burst into the lab, face red with anger.

"PHILLIP COULSON, YOU SON OF A BITCH."

Uh oh.

"How dare you? Oh, you're in for it now, you…you idiot!" Tears started to streak down her face, making her mascara run. "Not only do I have to deal with _this _one almost dying," she said, motioning to Tony, "But then I have to deal with you pretending to die, and not even bothering to tell me about it! You…you jerk! I, I could just…." And then, she glommed onto Phil, sobbing into his chest, mascara bleeding onto his dress shirt.

"Oh G-d Phil, I just…I missed you! This year has been so hard….I-I almost died! He almost died…twice! It would have been so much easier to have you around! But no, you-you just go off and don't even tell me that you are alive!"

"I'm so sorry, Pepper," he said, holding her against his chest, his voice slow and sad. "I truly am. I wish I could have told you Pepper, but you were not supposed to know. Technically, my existence is…classified."

"You should have known better, Agent," Tony said. "Nothing is classified to Tony Stark."

Eventually, Pepper's sobbing subsided, and she broke away. She then promptly slapped Phil in the face.

The team gasped.

"Okay, sorry everyone. I'm done now." She said. Phil just smiled. _That_ was the Pepper he knew.

"So, Agent Coulson, you going to tell us how you've been, or am I gonna have to have Pepper slap it out of you?"

"Before I tell you, Stark, I believe you have something to tell me first. How did you figure out I was still alive? Not even Romanoff and Barton know."

"Alright, alright. I guess that's fair. So, it all started when I was doing my bi-weekly hack of SHIELD…"

At that Skye blurted out "Go hackers!" And gave Tony a high-five. Ward rolled his eyes, but Tony smiled approvingly and continued with his story.

"So as I was saying, I was doing my bi-weekly SHIELD hack when I stumbled upon a particularly interesting chat between Nick Fury and an Agent named Blake. Fury started by talking about a collectible car named Lola, and then went on to say something about a certain team trashing a particularly expensive plane. I was intrigued, so I read on. Old one-eye was talking about how the leader of this team still believed that Fury owed him for quote 'what he did for me in New York,' and for (now, I think this was typed sarcastically because it was in italics) 'those precious, mint condition cards I ruined.' And then, my friends, it clicked. It was so obviously Coulson, with those precious Cap cards and the all the collectibles. So I put in a request to meet with Fury immediately, and naturally, I was declined. So, naturally, I tracked down his location and went to see him directly. Eventually, I got the answers that satisfied me, and I tracked down your airbus. And voila, here I am."

Coulson shook his head.

"I should have known something like this would happen. Have you told any of the others?"

"Nope. Fury told me that if I went that far he would cut off a certain part of my male anatomy, and it's a part I don't particularly want to give up." Phil rolled his eyes.

"Alright, I guess I would start giving introductions, but I think you've already met everyone. Wait…does anyone know where Agent May is?" The team looked at each other.

"Um...she said she was going out." Simmons said. "She didn't say where."

"Typical." Coulson said. "Alright, so do you two want a tour of the place?"

"Of course. But first, you need to tell me if you're still seeing that Cellist. She came to your funeral, but I was wondering if maybe you've told her about your resurrection." Skye raised her eyebrows amusedly at the mention of a Phil's former girlfriend.

'Boy,' Skye thought, recalling their encounter with Camilla Reyes, 'AC sure has a lot of girlfriends.'

"Oh, Wanda? I haven't seen her in ages."

"Aww, that was too bad, I liked her." Coulson smiled again, remembering Pepper's affinity for the cellist. Wanda was always the charmer. Before he could respond though, he heard a yawn from one of the team members.

"Why don't I take you and Tony on that tour now? I think if you've met everyone, they can probably go back to their bunks. They're all really exhausted… we have had a pretty busy past couple of days."

"Don't worry sir," Ward said. "We're not that tired…"

"Oh, come on, Kiss-ass." Tony said. "You've got bags under your eyes that could hold Fury's ego. Go to bed."

Ward began to protest and sputtered a little. Normally, he would have been a bit more collected, but exhaustion had taken its toll on even him.

"Aw, don't get your panties in a twist, I'm just messing with you. Now run along, leave the adults alone."

Ward turned red with anger, but left with whatever dignity he still had left.

"You guys are awesome!" Skye said. "AC, can we have them over here all the time?" Skye then left abruptly with the question still hanging, unwilling to get a negative answer.

"Mr. Stark, I know we have to leave, but is there anyway we could pick your brain about anti-matter limitations sometime in the future?" Fitz said nervously.

Stark pulled a pen out of his pocket, grabbed a pad out of Fitz's hand, and scribbled something down.

"That's my personal email. Send me a message if you have a question. But don't go giving it out to people…If you do, I'll track you down myself."

"Yes, sir. Thank you very much, sir." FitzSimmons said in unison, and scurried out of the lab.

"Talented kids, those two." Tony said, after they had left. "And that Skye girl knows what she's doing with computers. You got lucky with this team, Coulson. You've got a lot of good people. That Ward kid's kind of stiff, but I guess you need someone like that to balance them out. And he definitely has a good heart." Coulson smiled.

"Nice to know you approve, Stark," he said sarcastically. "Just wait till you meet May…Though I doubt she'll welcome you as enthusiastically." Stark waved it off.

"Nonsense. I have a way with the ladies. Tell 'im, Pep." Pepper just shook her head. Yet again, Coulson smiled. He had missed this.

"Alright, why don't we start the tour?" Phil said, and the trio began to walk, Tony chatting all the way. As he led them into his office, showing them his collectibles, Tony said something that took Coulson by surprise.

"You know, Agent, Cap was actually pretty affected by you dying." Phil was shocked.

"W-what? W-why? I-I barely met the guy…And I'm pretty sure he though I was a bit odd." Then he mumbled to himself. "I watched you sleep…what was I thinking?"

"Rogers felt kind of bad that he never signed your cards. He though it would have been the least he could do. I mean, what you did, although it was extremely, extremely, extremely idiotic..."

"Extremely moronic." Pepper added

"…As I was saying, even though what you did was flat out foolish, it was pretty brave, I got to say."

Phil didn't know what to say. Not only had he just found out that his idol actually cared about him, but Tony Stark had just called him brave. It wasn't even that Phil was seeking Tony's approval, it was just, that kind of thing coming from Stark was impressive.

Suddenly, he got that pang in his chest, that one of sadness and longing that had plagued him after he had returned from magical Tahiti. Nothing had seemed to hurt in Tahiti (nothing emotional, anyway), but straight away when he got back his emotions had crashed over him like a tidal wave. He really wanted to tell someone he was alive…He wanted to see Romanoff and Barton again (he had been there handler, after all). He wanted to go out to lunch with Pepper again. He wanted Cap to sign his cards. He loathed to admit it, but he even missed Stark's sassy sense of humor. So many times he had squashed these feelings down, knowing they were not the kind of emotions that would let him move on. Ever since last week, with that whole fire-man incident, he had felt them bubbling under the surface again, but this time he had tried to use them as a positive things, trying to channel them into helping him become that new person him and Melinda had talked about. But now they were back again, fiery as ever.

"Hey Phil, are you okay?" Pepper asked, concerned.

"What?" Phil said, pulling himself out of thought. "Yeah, yeah I'm fine."

"So, speaking of being fine, how's that new ticker holding up?" Now that really took Coulson by surprise.

"What? What do you mean 'new ticker'?"

"Oh, I guess I was wrong then. See, the Stark medical line has been testing these new artificial hearts, powered by little arc reactors. SHIELD put an order in for one months ago. I didn't think much about it at first, but when I found out you were alive, I just thought they probably were going to use it on you…" Tony explained.

"Oh. Actually, that may be possible. All SHIELD told me was that I died for about 8 seconds, and then they shipped me off to Tahiti to heal." Coulson said. When Stark had explained it, it seemed logical. It sure did explain the off feeling he had been having.

"So you didn't even notice? Wow. Well, that's the biggest customer endorsement I'm probably going to ever get. Mind if I use that in the brochure?"

"Yeah...whatever…"Coulson said, but in truth he hadn't really been listening. He was much too distracted by this newfound realization. It made so much sense, yet he didn't want it to be true. Although he knew he had changed, had he really changed that much? That he didn't even have his own heart anymore? It freaked him out. Phil had always been proud of his humanity, and ever since New York, he had felt it slowly being stripped away. Now even his heart wasn't human. What else had SHIELD done to him?

"Hey, Phil?" Once again, Pepper broke his train of thought, but he was grateful. He didn't want to think about this much, at least not right now.

"Oh, what?" He tried to recall what Stark had been saying to him. "Oh, yeah, Mr. Stark. You can use it if you want, but only if you leave my name out of it."

"Sure thing." Although Tony seemed to notice nothing, Pepper was staring at him with a concerned look in her eye. He tried to wave her off with a smile, but the worry still remained.

"Hey Coulson," Tony said, breaking Phil and Pepper's eye conversation. "This is a decent plane you got here, but you should really let me trick it out. I could do all kinds of kick-ass stuff with this plane. Take it to the next level, you know."

"I do not think that is necessary, Mr. Stark," said a voice echoing from the shadows, and Melinda May stepped out from the darkened corridor ("What is it with SHIELD and dark corridors?" Coulson thought to himself, bemused).

"Ah, Agent May, you have returned. As you have probably already figured out, we have visitors." May nodded. She ignored Stark, who had extended his hand expectantly, and went over to Pepper.

"Nice to meet you, Ms. Potts." Coulson, not for the first time that day, was taken by complete surprise. This was not May's style. She was not the hand-shakey type of person. She must have either really respected Potts, or really wanted to get under Stark's skin. Coulson suspected it was a mix of both.

"Likewise, Ms…"

"Just call me Melinda." May said.

"Well then, nice to meet you Melinda." Pepper gave her a warm smile.

"Um, hello Melinda. You can call me Tony if you want." Interrupted Tony, trying to pour on that classic Tony Stark charm, but evidently, it did not work. She nodded at him curtly.

"I've heard a lot about you, Mr. Stark. Congratulations on New York. You did a brave thing." She turned to Coulson. "I'm going to go sleep. See you in a couple of hours." And with that, she left.

"Well what was that about?" Tony asked.

"Don't know." Over the years, Coulson had realized there were a lot of things May did that he wouldn't understand, and that questioning it and/or thinking about them was pointless.

After that, the tour went relatively smoothly, and before he knew it, Coulson was struggling to keep his eyes open.

"Tony, I think we should go. Phil looks exhausted. We should let him rest."

"Okay, but Agent C, just warning you, this won't be the last visit. You're not going to get off the hook this easy."

"Yeah. Phil, we have to make lunch plans ASAP." Phil yawned happily. "Looking forward to it, Pepper."

"Pepper, go ahead, I think I left something it the lab."

"Okay, see you in a few." Before she left, she went over to Phil and embraced him, and gave him a friendly kiss on the cheek. "Goodbye for now, Phil."

"Bye Ms. Potts." He said, a touch of sadness resonating in his voice.

Once she left, Tony turned to him.

"I didn't really leave anything in the lab. I-I just wanted to tell you something." Well, this was certainly different, Coulson thought to himself.

"I've almost died about 4 times so far, and every one of them did something to me. I know that you did actually die, and I'd like to think that because of my experience I understand a bit what that's like. So, I just wanted to tell you that if you ever want to, you know, talk about it, I'm here. I-I think it wouldn't just be good for you, but for me too, you know?"

Ahh, everything made sense now. He had noticed Tony had been treating him much more mildly than before this whole time, and this was why. Coulson smiled at him, feeling a very honest sense of affinity for the other man.

Coulson knew he would never be able to recover the person he was before, but slowly his loneliness was beginning to lift, and he was realizing that he was not alone in his struggle. Not only did he have May to rely on, but now he had Tony as well.

It was starting to seem that not only the men themselves had changed, but their relationship had too. And this change, Coulson was sure, was for the better.

"Thank you very much, Mr. Stark. I will gladly take you up on that offer."

Tony smiled at him then, his grin a mix of sadness and hope.

"See you around, Agent. Take care of yourself, will you?"

"I will. Don't drive Pepper so nuts, okay?"

Tony smiled once more, this time mischievously.

"I'll try my best," was his final answer, but somehow Coulson knew he wouldn't try at all. And for once in his life, he didn't think that was a bad thing.


	2. Epilogue: Ominous Partings

Here is the epilogue...The ending is a bit ambiguous, don't kill me :) There is a possibility I might do a sequel, we'll see...

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><p>"Well, it was sure good to see Phil again. I'm glad he seems to be doing well." Pepper said, sitting down across from Tony on the jet.<p>

"Yeah, it was." Tony said, but truly he had other things on his mind.

"Hey Pep, I have a question for you."

"What is it?"

"Did you notice that something is different about Coulson? I mean, of course he's different, for G-ds sake he actually died. But did you notice that he…he just felt different? Something about him just didn't _feel _right."

"I…Yes, I did, did notice that," She admitted. "I thought it might just have been that new heart of his, but I think it's something else." Tony nodded, his suspicions confirmed.

"I wonder what the hell SHIELD did to him."

They sat for a while in silence, pondering the frightening matter.

Finally, Pepper spoke up.

"I don't think we should think about this right now, Tony. What's important is that Phil is happy, we are happy, and that SHIELD, whatever they did to him, would not want to hurt him."

Tony nodded, and Pepper started to get up.

"I'm going to go get something from the kitchen, you want anything?"

Tony shook his head, still in thought.

"Don't worry too much, okay Tony?" she said, and gave him a kiss.

The minute Pepper was out of the room, Tony pulled out his StarkPhone™.

"Jarvis, are you done with that scan I asked you to run on Coulson?"

"Yes, sir." The AI's infallible voice answered.

"Show me the results."

"I'm afraid I cannot do that, sir."

"And why is that?"

"The results have been erased, sir"

"Erased?" Tony said, confused. "By who?"

"An external protocol. Apparently they contain classified information that you are not allowed to access."

Tony was taken by surprise. He was sure his firewall was absolutely unreachable. Evidently, whatever was going on with Coulson was top, top secret. So secret SHIELD was expending a great amount of effort to make sure absolutely no one could find it out.

"This can't be good," Tony mumbled to himself.

And although he didn't know it, Tony Stark could not have been more right.


End file.
